Phd Position in Molecular Control of

6 maanden geleden

Utrecht, Nederland Universiteit Utrecht Voltijd

The immune system helps plants resist pathogen infections and has been well studied. However, it becomes increasingly clear that enhancing defense comes at a cost, as plants slow down growth even if the infection is successfully combatted. In this project, you will investigate the poorly understood process of how plants control their growth during and after an immune response. You will capitalise on the available extensive lettuce gene expression and high-throughput phenotyping datasets.

**Your job**:
Current projections show that the incidence of diseases on crops will increase in the coming decades, and thus, conceptually new strategies, beyond strengthening the immune system, are needed to ensure the resilience of future crops. It turns out that plants slow down their growth during and after an immune response regardless of the disease intensity. However, how these growth processes are regulated in plants is unclear. In this curiosity-driven PhD project, you will uncover the genetic and molecular basis of plant growth during and after an immune response. With this knowledge, one could develop approaches that reduce this tradeoff in crop growth. You will primarily work with lettuce (_Lactuca sativa_), but conservation of the deduced concepts can be investigated in other plant species, such as _Arabidopsis thaliana_.

Your project will capitalise on two types of datasets generated during the LettuceKnow programme. The first dataset includes large and dense time-course RNAseq experiments, where we activated the lettuce immune system and tracked the transcriptome changes over several hours. The second dataset includes high-throughput digital phenotyping data for the growth of ~180 lettuce varieties in the presence of defense hormones and after their removal (the recovery phase). This dataset was obtained with the Netherlands Plant Ecophenotyping Center (NPEC).

In the first phase of the project, you will utilise bioinformatics, genome-wide association mapping (GWAS), and machine learning techniques to identify new players of plant growth during and after an immune response. You will validate the genetic leads, such as transcription factors (TFs), identified in our earlier research. In the second phase of the project, you will work on the functional validation and characterization of the identified regulators of immunity-conditioned growth (e.g., TFs) using CRISPR-Cas gene editing and alteration of gene expression in lettuce and Arabidopsis. For selected targets, you will use quantitative proteomics and chromatin-protein interaction assays to gain insights into the activity of protein complexes driving growth during and after an immune response. Similarly, high-throughput digital phenotyping of mutants and overexpression lines in NPEC can be used to investigate their impact on inferred regulatory pathways.

We currently have another PhD position on growth-immunity tradeoffs available in Dmitry Lapin’s team. For more information about this position, check out our website.

**Your qualities**:
We are looking for a collaborative, enthusiastic, and curiosity-driven colleague who:

- has a completed MSc degree or is about to get an MSc degree in molecular and/or computational biology;
- has an affinity to experimental (plant) biology research;
- has demonstrated skills in either or both computational and molecular biology research;
- wants to learn, deploy, or even develop new methods of computational and molecular biology research.

**Our offer**:

- We offer:

- a position for 4 years;
- a gross monthly salary between €2,770 and €3,539 in the case of full-time employment (salary scale P under the Collective Labour Agreement for Dutch Universities (CAO NU);
- 8% holiday pay and 8.3% year-end bonus;
- a pension scheme, partially paid parental leave and flexible terms of employment based on the CAO NU.

In addition to the terms of employment laid down in the CAO NU, Utrecht University has a number of schemes and facilities of its own for employees. This includes schemes facilitating professional development, leave schemes and schemes for sports and cultural activities, as well as discounts on software and other IT products. We also offer access to additional employee benefits through our Terms of Employment Options Model. In this way, we encourage our employees to continue to invest in their growth. For more information, please visit Working at Utrecht University.

**About us**:
A better future for everyone. This ambition motivates our scientists in executing their leading research and inspiring teaching. At Utrecht University, the various disciplines collaborate intensively towards major strategic themes. Our focus is on Dynamics of Youth, Institutions for Open Societies, Life Sciences and Pathways to Sustainability. Sharing science, shaping tomorrow.

At the Faculty of Science there are 6 departments to make a fundamental connection with: Biology, Chemistry, Information and Computing Sciences, Mathematics,

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